Plant cells, unlike animal cells, are surrounded by a relatively thin but mechanically strong cell wall. The plant cell wall is essential for many processes in plant physiology and plant development. Because of its tough outer coating, the plant cell wall provides a cellular exoskeleton that controls cell shape and allows a high turgor pressure.
Plant cell walls are composed of a complex mixture of polysaccharides and other polymers that are organized into a network linked by covalent and noncovalent bonds. Plant cell walls also contain structural proteins, enzymes, phenolic compounds, and other materials that can modify the wall's chemical and physical structure. While the appearance and architecture of cell walls varies greatly among different cell types, cell walls are commonly classified into two major types: primary walls and secondary walls.
Primary cell walls are formed by growing cells and are generally unspecialized. Primary cell walls have a similar structure and composition that is present throughout diverse cell types; generally, primary walls are composed of approximately 25% cellulose, 25% hemicellulose, 35% pectin, and about 10% structural protein. In the primary cell wall, cellulose microfibrils, which contribute to the wall's strength, are embedded in a matrix. The individual cellulose chains that comprise the microfibril are closely aligned and form a crystalline structure that is relatively inaccessible to enzymatic digestion. Thus, cellulose is very stable and only degrades during specific developmental stages, such as abscission and senescence. The cell wall matrix is composed of two polysaccharide types, hemicellulose and pectin, along with a small concentration of structural proteins. The matrix is generally well-hydrated, and the matrix hydration state determines the physical properties of the wall.
Secondary cell walls form after cessation of cell growth and enlargement. Unlike primary cell walls, secondary cell walls can adopt highly specialized structures and compositions. For example, xylem cells, such as those found in wood, have thickened secondary walls that are strengthened by lignin.
Recently, several plant cell wall proteins have been identified. For example, polynucleotide sequences encoding the following plant cell wall proteins have been identified: α-amylase, Arabinogalactan, Brassinosteroid-regulated Protein Precursor, β-1,3-endoglucanase, β-1,3-glucanase, β-D-glucan exohydrolase, β-glucosidase, β-xylosidase, Calnexin, Calreticulin, Cellulase, Cellulose synthase, Chitinase, Dirigent, Expansin, Extensin, Galacturan 1,4-α-galacturonidase, Glucose-1-phosphate adenyltransferase, Glycosyl transferase, Glycosyl hydrolase, Glycoside hydrolase, Hexose pyrophoshorylase, Hydroxyproline-rich proteins, Mannose-6-Phosphate Isomerase, Mannose-1-Phosphate Guanylyltransferase, Nucleotidyl transferase, Pectins, Pectin Methylesterase, Phosphomannomutase, Plant disease resistance response protein, Polygalacturonase, Pollen allergen/expansin, Starch Branching Enzyme, Starch Synthase, Sucrose-phosphate synthase, Sucrose synthase, Syringolide-induced protein, UTP-glucose-1-phosphate uridylyltransferase, Xyloglucan endotransglycosylase, Xyloglucan synthase, Xyloglucan: xyloglucosyl transferase, and Yieldin.
While much is known about the structure and metabolic regulation of various cell wall proteins, very little is known about their functions and intercellular interactions. Additionally, the multigenic control of a plant phenotype presents difficulties in determining the genes responsible for a given phenotype. One major obstacle to identifying genes and gene expression differences that contribute to phenotype in plants is the difficulty with which the expression of more than a handful of genes can be studied concurrently. Another difficulty in identifying and understanding gene expression and the interrelationship of the genes that contribute to plant phenotype is the high degree of sensitivity to environmental factors that plants demonstrate.
There have been recent advances using genome-wide expression profiling. In particular, the use of DNA microarrays has been useful to examine the expression of a large number of genes in a single experiment. Several studies of plant gene responses to developmental and environmental stimuli have been conducted using expression profiling. For example, microarray analysis was employed to study gene expression during fruit ripening in strawberry, Aharoni et al., Plant Physiol. 129:1019-1031 (2002), wound response in Arabidopsis, Cheong et al., Plant Physiol. 129:661-7 (2002), pathogen response in Arabidopsis, Schenk et al., Proc. Nat'l Acad. Sci. 97:11655-60 (2000), and auxin response in soybean, Thibaud-Nissen et al., Plant Physiol. 132:118. Whetten et al., Plant Mol. Biol. 47:275-91 (2001) discloses expression profiling of cell wall biosynthetic genes in Pinus taeda L. using cDNA probes. Whetten et al. examined genes which were differentially expressed between differentiating juvenile and mature secondary xylem. Additionally, to determine the effect of certain environmental stimuli on gene expression, gene expression in compression wood was compared to normal wood. A total of 156 of the 2300 elements examined showed differential expression. Whetten, supra at 285. Comparison of juvenile wood to mature wood showed 188 elements as differentially expressed. Id. at 286.
Although expression profiling and, in particular, DNA microarrays provide a convenient tool for genome-wide expression analysis, their use has been limited to organisms for which the complete genome sequence or a large cDNA collection is available. See Hertzberg et al., Proc. Nat'l Acad. Sci. 98:14732-7 (2001a), Hertzberg et al., Plant J., 25:585 (2001b). For example, Whetten, supra, states, “A more complete analysis of this interesting question awaits the completion of a larger set of both pine and poplar ESTs.” Whetten et al. at 286. Furthermore, microarrays comprising cDNA or EST probes may not be able to distinguish genes of the same family because of sequence similarities among the genes. That is, cDNAs or ESTs, when used as microarray probes, may bind to more than one gene of the same family.
Methods of manipulating gene expression to yield a plant with a more desirable phenotype would be facilitated by a better understanding of cell wall gene expression in various types of plant tissue, at different stages of plant development, and upon stimulation by different environmental cues. The ability to control plant architecture and agronomically important traits would be improved by a better understanding of how cell wall development effects plant cell development and morphology.
Accordingly, there exists a need for efficiently identifying genes that regulate plant cell wall synthesis and development.